I have written a program in C to calculate deformation energy scores on DNA duplexes from 3DNA output, based on X-ray averages and force constants at the base-pair or base-pair step level. This program gives not only the total deformation energy but also its components. I attach an archive containing the program as well as 3DNA output files to perform two tests:

The above note refers to the C++ program written by Marc Parisien (University of Montreal, Canada) for calculating deformation energies at the base-pair or dinucleotide step level. Since the referred to URL is now dysfunctional, I have consolidated all the related information here.

-- Xiang-Jun

Email message from Marc Parisien on the C++ program ('EnergyPDNA.C' and the associated header file 'EnergyParams.h' are attached below)

We now have the base-pair level deformation energies!! I have updated the program; see attached files :-)

I have decoupled the energy calcs since there is the possibility of coupled interactions between base-pairs and base-steps parameters...(like Propeller-Rise, etc) another article maybe for that ;-)It would generate a huge matrix though: 12 x 12 (6 params for bases + 6 params for steps = 12 total params).

I have also change the energy calcs loops from:

1) i = 0 to 5 // the 6 parameters j = 0 to 5

to

2) i = 0 to 5 j = i to 5

because in 1) the i-j and j-i are counted twice, except for i-i, so it is not correct to then simply divide by 2. in 2) the i-j are counted singly, even for i-i.

> What's the energy reported? is it the energy that you need to apply to the> system to obtain a given DNA deformation with a given sequence?It is a deformation energy (units are kcal/mol, I think) based on population preferences: E = -RT ln( P ) where P is the probability offinding the sample in that conformation. This deformation energy reachesback to Go where he analyzed the protein helix deformations (I don'thave that reference). I suggest that you imperatively read the 2 articlesmentionned in the "credits" section of the program (in the main() routine).

> Do you need full-detail PDB coordinates of the DNA or the backbone is enough?> Thanks for your feedback and for the code!!Unfortunately, you need the full DNA since the energies come from the side-chain conformations. You will have to launch the 3DNA program beforecalculating the energies.

The energies reported here are not to be confused with those reported by force-fields like AMBER or CHARMM... the energies here are those only from population samples! You would have to do a thermodynamic cycle to obtain the energy to apply to the system to obtain a given DNA deformation with a given sequence!

As an application of this program you can look at a DNA/Protein complex and do in-silico DNA mutations by changing the nature of the nucleotides but without modifying the DNA 3D structure... You can then select the bestDNA sequence for that particular DNA 3D structure...

Do not mix the 2 energies calculations: use my program with the "-s" option (the step energy) or with "-b" (the base-pairs energy)...

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.